Accumulation and deposition of sediments in waterbody affect the seepage capacity that could lead to improper water balance and results in the water level rise. .is study analysed the influence of sedimentation on seepage capacity in Lake Nakuru and the impact of sediment characteristics to the water seepage and the flow rate formation at the lake bed level. .e study was performed by sampling and analysing the sediment cores from two locations in the lake. .e sediment hydraulic properties, i.e., moisture and porosity, particle sizes, and hydraulic conductivity, were determined using the oven-drying method, sieve analysis, hydrometer analysis, and falling head tests, respectively. .e results showed that the lake sediment sample from location P1 had an average ratio of 39.38% for silty soil, 34.00% for clayey sediment, and 26.63% for fine-sand sediment particles with the maximum permeability coefficient of 3.37 ∗ 10− 5 cm/s, while the one from location P2 had an average ratio of 63.17% for sand, 20.17% for fine particles, and 16.67% for gravels with the maximum permeability coefficient of 0.010793 cm/s. .e hydraulic conductivity of sediment sample from location P1 and P2 increased along the core depth. .is could lead to the rise of water level due to the decreases of water movement induced from the sediment cementation in the top layers under the waterbody. Sedimentation affects Lake Nakuru water volume and water balance; hence, there is a need to control the inflow of sediment resulting from anthropogenic activities in the watershed.