Lake Naivasha and Lake Oloiden merged leading to the formation of an estuary. This occurrence may affect the water quality and phytoplankton. A study was conducted with the objective: to investigate seasonal changes in the water quality parameters and their effect on phytoplankton. Depth and secchi depth were measured while some water quality parameters were measured in situ using YSI Multiparameter meter and water samples were collected for laboratory analysis of chlorophyll-a, phosphates, nitrates and total suspended solids. Phytoplankton sample was collected; identification and counting were done under a compound microscope. The nutrients, depth, secchi depth, temperature, dissolved oxygen, salinity, conductivity, total dissolved solids and pH varied monthly. All the water quality parameters positively correlated with Chlorophyceae in Lakes Naivasha and Oloiden except dissolved oxygen, chlorophyll-a, depth and secchi depth that negatively correlated. There were seasonal changes in all the water quality parameters in Lakes Naivasha and Oloiden except the total suspended solids whose effects were in Midlake There were seasonal changes in all the water quality parameters in Lakes Naivasha and Oloiden except the total suspended solids whose effects were only in Midlake and Oloiden ST2. Euglenophyceae, Bacillariophyceae were not affected by water quality except the depth while the other families had varied effects from water quality in Lake Naivasha. All Lake Oloiden's phytoplankton families had varied effects from the water quality. Thus, the prevailing water quality affect phytoplankton