DESPITE OF IT'S ECONOMIC IMPORTANCE, THE DRAINAGE SYSTEM OF UGANDA HAS IT’S OWN SHORTCOMING AS FOLLOW:

Lakes like Nyamunuka in busenyi have caused air pollution due their bad smell .this leads to health hazard among people in area.

Wetlands such as Nabajuzi in Masaka, Lakes such as Mburoand ponds with stagnant water at kajjansi and seeta form breeding ground for pest and diseases e.g. Mosquitoes and snails that cause malaria and bilhazia respectively. This affects the health of people and therefore retarts the economic growth.
Lake Kyoga, Bisina and rivers like mayanja, Katonga and kagera have tendency of flooding and hence destroy the crops in the surrounding area. Flooding May also leads to human displacement and spread f water born diseases. In 1950’s Lake Albert flooded many landing sites

Such as Butiaba and wanseka destroying crops and animal.
The drainage system in form of Lake Victoria, Kyoga, Albert, George and athers act as a social and economic barrier between people on the opposite sides. For example Lake kyoga is a barrier between Nakasongola and Lwamanga in the south and lira in the north.
The drainage system suffers from toxt pollutants e.g. Lake Victoria polluted by industries at jinja and Luzira.many fish are therefore killed .the uncontrolled fishing may lead to depletion thereby limiting the economic importance of lakes and rivers

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Water as means of transport is risky in that, people are bound to drown. Many goods and people’s lives have been lost this way on Lake Victoria in wakiso, Lake Kyoga in Nakasongola
Lakes like Victoria encourage smuggling since there shared with other countries like Tanzania, Kenya and DR Congo. This has led to lots of government revenue necessary for development.

Lumbuye wetlands in Iganga and lakes such as Lake Victoria, Kyogaand wetlands in Mayuge also unsafe because they harbor dangerous animals like crocodiles which terrorize the neighboring villages by eating the people.
Theft and piracy is also common in lakes like Victoria, Kyoga because of inadequate security. This has led to loss of property and leads to poverty

Many rivers have rapid and falls e.g the Ssipi falls on river sipi, Murchison, Karuma and Bujangali on the Nile cannot therefore be used for navigation. Other rivers like Lumansi in Luwero are subjected water fluctuations and therefore are of less significancy.
Lakes such as Victorian in Wakiso have encourage growth of towns /landing sites such as kasensero landing sites with their associated evils like high crime rate , congestion, Prostitution etc.