The prognosis of hydronephrosis is extremely variable, and depends on the condition leading to hydronephrosis, whether one (unilateral) or both (bilateral) kidneys are affected, the pre-existing kidney function, the duration of hydronephrosis (acute or chronic), and whether hydronephrosis occurred in developing or mature kidneys.

For example, unilateral hydronephrosis caused by an obstructing stone will likely resolve when the stone passes, and the likelihood of recovery is excellent. Alternately, severe bilateral prenatal hydronephrosis (such as occurs with posterior urethral valves) will likely carry a poor long-term prognosis, because obstruction while the kidneys are developing causes permanent kidney damage even if the obstruction is relieved postnatally.

Hydronephrosis can be a cause of pyonephrosis - which is a urological emergency.

Hydronephrosis is the result of any of several abnormal pathophysiological occurrences. Structural abnormalities of the junctions between the kidney, ureter, and bladder that lead to hydronephrosis can occur during fetal development. Some of these congenital defects have been identified as inherited conditions, however the benefits of linking genetic testing to early diagnosis have not been determined. Other structural abnormalities could be caused by injury, surgery, or radiation therapy.

Compression of one or both ureters can also be caused by other developmental defects not completely occurring during the fetal stage such as an abnormally placed vein, artery, or tumor. Bilateral compression of the ureters can occur during pregnancy due to enlargement of the uterus. Changes in hormone levels during this time may also affect the muscle contractions of the bladder, further complicating this condition.

Sources of obstruction that can arise from other various causes include kidney stones, blood clots, or retroperitoneal fibrosis.

The obstruction may be either partial or complete and can occur anywhere from the urethral meatus to the calyces of the renal pelvis. Hydronephrosis can also result from the reverse flow of urine from the bladder back into the kidneys. This reflux can be caused by some of the factors listed above as well as compression of the bladder outlet into the urethra by prostatic enlargement or impaction of feces in the colon, as well as abnormal contractions of bladder muscles resulting from neurological dysfunction or other muscular disorders.

It has been estimated that VUR is present in more than 10% of the population. Younger children are more prone to VUR because of the relative shortness of the submucosal ureters. This susceptibility decreases with age as the length of the ureters increases as the children grow. In children under the age of 1 year with a urinary tract infection, 70% will have VUR. This number decreases to 15% by the age of 12. Although VUR is more common in males antenatally, in later life there is a definite female preponderance with 85% of cases being female.

The American Urological Association recommends ongoing monitoring of children with VUR until the abnormality resolves or is no longer clinically significant. The recommendations are for annual evaluation of blood pressure, height, weight, analysis of the urine, and kidney ultrasound.

Duplicated ureter is the most common renal abnormality, occurring in approximately 1% of the population.

Race: Duplicated ureter is more common in Caucasians than in African-Americans.

Sex: Duplicated ureter is more common in females. However, this may be due to the higher frequency of urinary tract infections in females, leading to a higher rate of diagnosis of duplicated ureter.

The evidence linking vitamin C supplements with an increased rate of kidney stones is inconclusive. The excess dietary intake of vitamin C might increase the risk of calcium oxalate stone formation, in practice this is rarely encountered. The link between vitamin D intake and kidney stones is also tenuous. Excessive vitamin D supplementation may increase the risk of stone formation by increasing the intestinal absorption of calcium; correction of a deficiency does not.

There are no conclusive data demonstrating a cause-and-effect relationship between alcoholic beverage consumption and kidney stones. However, some have theorized that certain behaviors associated with frequent and binge drinking can lead to dehydration, which can, in turn, lead to the development of kidney stones.

The American Urological Association has projected that global warming will lead to an increased incidence of kidney stones in the United States by expanding the "kidney stone belt" of the southern United States.

People with lymphoproliferative/myeloproliferative disorders who were treated with chemotherapy developed symptomatic kidney stones 1.8% of the time in one study.

Duplicated ureter or Duplex Collecting System is a congenital condition in which the ureteric bud, the embryological origin of the ureter, splits (or arises twice), resulting in two ureters draining a single kidney. It is the most common renal abnormality, occurring in approximately 1% of the population. The additional ureter may result in a ureterocele, or an ectopic ureter.

This requires drainage, best performed by ureteral stent placement or nephrostomy.

Stones can cause disease by several mechanisms:

- Irritation of nearby tissues, causing pain, swelling, and inflammation

- Obstruction of an opening or duct, interfering with normal flow and disrupting the function of the organ in question

- Predisposition to infection (often due to disruption of normal flow)

A number of important medical conditions are caused by stones:

- Nephrolithiasis (kidney stones)

- Can cause hydronephrosis (swollen kidneys) and renal failure

- Can predispose to pyelonephritis (kidney infections)

- Can progress to urolithiasis

- Urolithiasis (urinary bladder stones)

- Can progress to bladder outlet obstruction

- Cholelithiasis (gallstones)

- Can predispose to cholecystitis (gall bladder infections) and ascending cholangitis (biliary tree infection)

- Can progress to choledocholithiasis (gallstones in the bile duct) and gallstone pancreatitis (inflammation of the pancreas)

- Gastric calculi can cause colic, obstruction, torsion, and necrosis.

In kidney stones, calcium oxalate is the most common mineral type (see Nephrolithiasis). Uric acid is the second most common mineral type, but an "in vitro" study showed uric acid stones and crystals can promote the formation of calcium oxalate stones.

Pyonephrosis is sometimes a complication of kidney stones, which can be a source of persisting infection. It may also occur spontaneously. It can occur as a complication of hydronephrosis or pyelonephritis.

Up to 27 percent of individuals greater than 50 years of age may have simple renal cysts that cause no symptoms.

The female homolog to the male verumontanum from which the valves originate is the hymen.

Occurring at a rate between 1 in 10,000 to 1 in 50,000 with a male-to-female ratio of 2.3-6:1, bladder exstrophy is relatively rare. For those individuals with bladder exstrophy who maintain their ability to reproduce, the risk of bladder exstrophy in their children is approximately 500-fold greater than the general population.

Without diagnostic evaluation, the cause of UAB is unclear, as there are multiple possible causes. UAB symptoms can accurately reflect impaired bladder emptying due either to DU or obstruction (normal or large storage volumes, elevated post-void residual volume), or can result from a sense of incomplete emptying of a hypersensitive bladder (small storage volumes, normal or elevated postvoid residual volume). UAB potentially might also result from inaccurate perceptions of bladder function, such as in neurologic or psychiatric disease. DU itself is often linked to a weak detrusor muscle (impaired contractility), however this association is weak. Both UAB and DU have been associated with diminished sensitivity to bladder volumes rather than objective detrusor weakness, suggesting both symptoms (UAB) and function (DU) have a significant component of sensory dysfunction, leading to impaired bladder sensations and control (Smith et al., 2015).

The underlying contributors to UAB include neurologic disease, metabolic disease (e.g. diabetes), chronic bladder outlet obstruction (e.g. obstructive BPH or complications of anterior vaginal surgery), cognitive decline (such as with aging), psychiatric disorders, and adverse effects of medications. Additionally, structural abnormalities expanding the urinary reservoir beyond the bladder, such as massive vesicoureteral reflux or large bladder diverticulae, can result in UAB. While aging itself is often associated with UAB (and DU), there is scant evidence to support this claim.

Urethral strictures most commonly result from injury, urethral instrumentation, infection, non-infectious inflammatory conditions of the urethra, and after prior hypospadias surgery. Less common causes include congenital urethral strictures and those resulting from malignancy.

Urethral strictures after blunt trauma can generally be divided into two sub-types;

- Pelvic fracture-associated urethral disruption occurs in as many as 15% of severe pelvic fractures. These injuries are typically managed with suprapubic tube placement and delayed urethroplasty 3 months later. Early endoscopic realignment may be used in select cases instead of a suprapubic tube, but these patients should be monitored closely as vast majority of them will require urethroplasty.

- Blunt trauma to the perineum compresses the bulbar urethra against the pubic symphysis, causing a "crush" injury. These patients are typically treated with suprapubic tube and delayed urethroplasty.

Other specific causes of urethral stricture include:

- Instrumentation (e.g., after transurethral resection of prostate, transurethral resection of bladder tumor, or endoscopic kidney surgery)

- Infection (typically with Gonorrhea)

- Lichen sclerosus

- Surgery to address hypospadias can result in a delayed urethral stricture, even decades after the original surgery.

Depending on the cause, a proportion of patients (5–10%) will never regain full kidney function, thus entering end-stage kidney failure and requiring lifelong dialysis or a kidney transplant. Patients with AKI are more likely to die prematurely after being discharged from hospital, even if their kidney function has recovered.

The risk of developing chronic kidney disease is increased (8.8-fold).

The most important criterion for improving long-term prognosis is success of the initial closure. If a patient requires more than one closure their chance of continence drops off precipitously with each additional closure - at just two closures the chance of voiding continence is just 17%.

Even with successful surgery, people may have long-term complications. Some of the most common include:

- Vesicoureteral reflux

- Bladder spasm

- Bladder calculus

- Urinary tract infections

The use of bioengineered urethral tissue is promising, but still in the early stages. The Wake Forest Institute of Regenerative Medicine has pioneered the first bioengineered human urethra, and in 2006 implanted urethral tissue grown on bioabsorbable scaffolding (approximating the size and shape of the affected areas) in five young (human) males who suffered from congenital defects, physical trauma, or an unspecified disorder necessitating urethral reconstruction. As of March, 2011, all five recipients report the transplants have functioned well.

A renal cyst or kidney cyst, is a fluid collection in or on the kidney. There are several types based on the "Bosniak classification". The majority are benign, simple cysts that can be monitored and not intervened upon. However, some are cancerous or are suspicious for cancer and are commonly removed in a surgical procedure called nephrectomy.

Numerous renal cysts are seen in the cystic kidney diseases, which include polycystic kidney disease and medullary sponge kidney.

Mortality after AKI remains high. Overall it is 20%, 30% if the patient is referred to nephrology, 50% if dialyzed, and 70% if on ICU.

If AKI develops after major surgery (13.4% of all people who have undergone major surgery) the risk of death is markedly increased (over 12-fold).

Posterior urethral obstruction was first classified by H. H. Young in 1919. The "verumontanum", or mountain ridge, is a distinctive landmark in the prostatic urethra, important in the systemic division of posterior valve disorders:

- Type I - Most common type; due to anterior fusing of the "plicae colliculi", mucosal fins extending from the bottom of the verumontanum distally along the prostatic and membranous urethra

- Type II - Least common variant; vertical or longitudinal folds between the verumontanum and proximal prostatic urethra and bladder neck

- Type III - Less common variant; a disc of tissue distal to verumontanum, also theorized to be a developmental anomaly of congenital urogenital remnants in the bulbar urethra

Dewan has suggested that obstruction in the posterior urethra is more appropriately termed congenital obstructions of the posterior urethral membrane (COPUMs), a concept that has come from an in-depth analysis of the historical papers, and evaluation of patients with a prenatal diagnosis that has facilitated video recording of the uninstrumented obstructed urethra. The congenital obstructive lesions in the bulbar urethra, named Type III Valves by Young in 1919, have been eponymously referred to as Cobb's collar or Moorman's ring. For each of the COPUM (Posterior Urethra) and Cobb's (Bulbar Urethra) lesions, the degree of obstruction can be variable, consistent with a variable expression of the embryopathy. The now nearly one hundred year old nomenclature of posterior urethral valves was based on limited radiology and primitive endoscopy, thus a change COPUM or Cobb's has been appropriate.

Cystinuria is an inherited autosomal recessive disease that is characterized by high concentrations of the amino acid cystine in the urine, leading to the formation of cystine stones in the kidneys, ureter, and bladder. It is a type of aminoaciduria.

Underactive Bladder Syndrome (UAB) describes symptoms of difficulty with bladder emptying, such as hesitancy to start the stream, a poor or intermittent stream, or sensations of incomplete bladder emptying. The physical finding of detrusor pressurization of insufficient strength or duration to ensure timely and efficient bladder emptying is properly termed "detrusor underactivity" (DU) (Abrams et al., 2002). Historically, UAB and DU (as well as others such as 'bladder underactivity') have been often used interchangeably (Rigby D, 2005), leading to both terminologic and pathophysiologic confusion.

Patients with UAB have a diminished sense of bladder filling and consequently are often found to have DU as an underlying finding, however bladder outlet obstruction and less frequently volume hypersensitivity ("OAB") can be associated with UAB symptoms (Chapple et al., 2015).