Increasing demand for freshwater in arid regions with chronic water shortage calls for expansion of water storage for drought periods while protecting storage from evaporative losses. A cost‐effective and scalable method for evaporation suppression uses floating elements; however, little is known regarding biochemical and water quality effects under these covers. Two identical reservoirs with area of 25 m2 and depth of 2 m were used to investigate the influence of floating covers on water quality parameters for a period of one year (2019–2020). One of the reservoirs was covered with Styrofoam discs, and results were compared with the uncovered one. Results showed that the evaporation suppression efficiency of floating discs gradually decreased from 80% in spring to about 60% in winter. The comparison between reservoirs revealed that the presence of floating covers decreased pH, electrical conductivity (EC), total dissolved solids (TDS) and dissolved oxygen by 11%, 11%, 15% and 36%, respectively. We observed an increase in nitrate (30%), phosphate (27%) and ammonia (95%) concentrations in the covered reservoir. Results also demonstrated more concentration of biological populations such as algae and protozoa in the uncovered reservoir. The findings highlight improvement of certain water quality parameters in covered reservoirs such as EC and TDS with potential impacts on irrigation systems and soil health and salinity constraints.