Freshwater ecosystems are subject to anthropogenic contaminants. This study aimed at assessing waste management stratagem by the local population and implications on water abiotic variables as well as phytoplankton species richness of the Ndongo stream, South-West Cameroon. For this purpose, 144 structured questionnaires were randomly administered to inhabitants around the stream to assess wastes management practices. Water and phytoplankton analysis was done in three selected sites. The mainstream of inhabitants (67%) dumped wastes in facilities provided by the Buea Council. The sorting of wastes before disposal was not common among respondents (72%). Recycling of wastes was done by only 37.8% of inhabitants. Half of the respondents (50.7%) claimed being ready to contribute financially for waste management while 81.2% said they were aware of the consequences of poor waste management. The main source of domestic water in the area was tap water (89.6%) and the Ndongo stream was mainly utilised for washing clothes (47.9%). Water abiotic variables that exhibited significant spatial trends included conductivity, TDS, velocity, width, depth and flow rate. There was no significant difference in the spatial distribution of temperature, pH, salinity and dissolved oxygen. The phytoplankton community was made of 36 species distributed in 37 families. Taxa such as Lynbya sp., Oscillatoria sp. and Closterium sp. were found in all the sampling sites, making them resident species of the stream. The sampling site at the lower course of the stream had the highest phytoplankton species richness. The highest algal pollution index was found in site 3at the lower course of the stream. Species richness had a positive and non-significant correlation with temperature, conductivity, TDS, salinity, velocity, depth and discharge. Water pH, dissolved oxygen and width had a negative and non-significant correlation with species richness. The local population should be educated on wastes management and its implications on the environment.