Broad applications of Unmanned Aerial Systems (UAS) have emerged over the past decade. Estimation of water quality parameters of surface water sources is among the many applications of the UASs. Water resources are observed to be deteriorating over the past decades putting a threat to future availability of clean, portable water to future generations. Thus, the aim of this paper was to estimate and evaluate spatial variations of optical and non-optical water quality parameters for Naperi river within the city of Blantyre whose condition is speculated to be deteriorating. Aerial images were captured in April, 2024 with 80% overlaps along the river using DJI Mavic 2 pro. A flying height of 80m above the ground was utilised yielding a ground sampling distance of 2cm. Total Nitrogen, Total Phosphorous, Chlorophyl, Total Suspended Solids, Secchi Disk Depth were estimated from the captured images using existing published models. Chlorophyll is observed to have 0 mg/L, 1280mg/L, 275mg/L, 171mg/L as minimum, maximum, average and standard deviation respectively. Total Nitrogen is observed to have 1.456mg/L, 160.418mg/L, 63.450mg/L and 12.245mg/L as minimum, maximum average and standard deviation respectively. Secchi Disk Depth (water clarity) water quality parameter values ranged from 62.226cm to 458cm with an average and standard deviation of 163.673cm and 32.877cm respectively. Total Suspended Solids had minimum and maximum values of 519.713mg/L and 1149.577mg/L respectively. The average and standard deviation of 662.473mg/L and 54.582mg/L respectively. The results show different levels of water quality within and among the parameters. The study has demonstrated that cutting edge technologies like Unmanned Aerial Systems have the potential in monitoring aquatic systems from which mitigation measures against environmental degradation can be devised.