- Presence of water falls and rapids like Karuma on R. Nile
- Presence of wter weed/hythnith like on L. Kyoga and Victoria
- Existence of swamp vegetation on the fringes of lakes and rivers like Mpologoma, L. Kyoga, etc.
- Shallowness of some rivers like Katonga and Kagera
- Steep gradient/escarpment like on L. Albert.
- Narrowness of some rivers like Kafu and Sezibwa
- Reduction in water levels during drought seasons like on L. George.
- Strong winds/storms on lakes like Victoria
- Strong currents/tidal range which cause accidents like on L. Albert.
- Presence of dangerous wild animals like crocodiles at Kazinga channel.
- Presence of rock out crop in lakes like L. Victoria
- Floods due to heavy rains destroying ports like Bukakata on L. Victoria.
- Suds/floating islands on l. Wamala and Kyoga.
- Poorly developed transport network linking to ports like Nyendo-Bukakata road.
- Remoteness of some water bodies like Edward
- Limited capital to purchase modern vessels like on R. Nile
- Inadequate skilled labour to handle the sector on L. Victoria ports like Port Bell
- Limited government support
- Low levels of technology in ship building and maintenance.
- Competition for cargo and passengers from other forms of transport.
- Poorly developed port handling facilities.
- Political instabilities and piratess
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