Accelerated aging and eutrophication of water resources is a world menace attributed to influx of nutrient rich sediment from its catchment, resulting in poor water quality and shifts in ecological dynamism. Nyanza Gulf is a paramount source of livelihood, portable water, and of service to the rich biodiversity making it indispensable to the entire Lake Victoria watershed ecosystem. This water resource has been deteriorating over the past decades as a consequent of anthropogenic socio-economical activities. This has effectuated an increase in phytoplankton and hydrophyte colonies. The objective of this study was to track the quality and quantity of sediment inundation into the gulf considering the catchment micro-basins processes and influence of human socio-economical activities. Using Quantum Geographic Information System (QGIS) as an interface to Soil and Water Assessment Tool (SWAT) with input of satellite digital elevation model (DEM), local rainfall, soil and land use data sets were utilized to determine the daily variability in sediment and nutrient loads from five major river basins. The SWAT model was successfully calibrated, and the performance validated with observed hydrological and water quality data. The model achieved identification of seasonal water quality budget filling in knowledge gaps about the catchment. River Nyando, Sondu-Miriu, Awach-Kibuon, Awach-Tende and Kibos discharge sediment loads of 3.91, 1.6, 1.18, 1.06 and 0.78 tons/ha respectively. Total suspended solids (TSS) concentration of up to 578mg/L on average daily is discharged by River Awach-Kibuon. This was associated with intense agricultural activities (>54% of the entire basin) on steep slopes (average 12.97) with Acrisols (15%of the basin) soils that is prone erosion. Poorly managed range-bush land that covers about 10% of this basin also contribute significantly to the TSS yield. River Kibos discharge least TSS concentration of 144.43 mg/L in comparison with other rivers mainly due gentle slope falling into a plain, low erodible Cambisols (covers 20% of the basin) and Ferralsols (10%) as well as Nanga forest effect at its exit. River Awach-Tende and Awach-Kibuon on average discharge 1.67 mg/L and 1.58 mg/L respectively of Total Nitrogen (TN) daily. This was linked to intensive farming on poorly managed dominant Phaeozems and Acrisols that are susceptible to leaching. River Sondu-Miriu is the least contributor with a daily average of 1.1101 mg/L dominated with low leached Nitisols. The bay receives highest Total Phosphorus (TP) loads from River Nyando with daily average of 0.3699 mg/L alluded to high biomass production in the basin and Sondu-Miriu least with 0.0288 mg/L. The fluctuation of nutrients and sediment fluxes correlated positively with rainfall events. The long rainfall season with average regular storm events in March to June yield highest monthly loads as compared to short rainfall season (September to November) with isolated intense storm events over a shorter time. The study depicted poor water quality discharged into the gulf throughout the year by the 5 major basins to be above average of conventional ecological healthy basins.