Maintaining optimal water quality in reservoirs is a global challenge, particularly in arid or semi-arid regions where these water bodies are critical yet vulnerable ecosystems. A prerequisite for effective environmental preservation is the precise delineation of spatiotemporal and vertical variability in water-quality variables, especially across a complete seasonal cycle. This study was therefore designed to systematically investigate and document the detailed spatial and seasonal variation in the water quality of the Wadi Dayqah Dam (Oman). This characterization was based on a robust, year-long dataset spanning 19 separate sampling occasions and incorporating high-resolution depth profile measurements of temperature, dissolved oxygen (\(\:\text{D}\text{O}\)), oxidation-reduction potential (\(\:\text{O}\text{R}\text{P}\)), pH, turbidity and chlorophyll-a from 20 distinct depth-profiling stations. Self-organizing map \(\:(\text{S}\text{O}\text{M}\)) was used to identify spatial zones, while thermal stratification dynamics were quantified using the Schmidt Stability Index (\(\:\text{S}\text{S}\text{I}\)) and the Thermocline Strength Index (\(\:\text{T}\text{S}\text{I}\)). This integrated approach combines high-resolution spatial clustering with complementary stratification metrics to reveal zone-specific water quality patterns typically obscured by single-point monitoring. \(\:\text{S}\text{O}\text{M}\) differentiated distinctly phased lacustrine, transitional, and riverine regions with spatial heterogeneity in water quality, with pronounced longitudinal gradients in temperature, \(\:\text{D}\text{O}\), turbidity, and chlorophyll-a across zones, an aspect traditionally overlooked by localized single-point, as opposed to distributed, observation. This spatial heterogeneity highlights the importance of zone-specific reservoir management strategies. On-site, observations revealed pronounced yearly patterns of thermal stratification and mixing, with the most intense and persistent stratification occurring in the lacustrine zone, where Schmidt stability reached a maximum of approximately 1144 \(\:\text{J}{\:\text{m}}^{-2}\). Notably, chemical stratification closely followed the temporal dynamics of thermal stratification, resulting in pronounced hypolimnetic anoxia in the deeper lacustrine waters, typically persisting from May to October. In contrast, suspended particulate matter and organic substances exerted a stronger control on turbidity and chlorophyll-a concentrations, with the latter reaching peak values of approximately 27 \(\:{\upmu\:}\text{g}\:\text{L}^{-1}\). Recurrent severe hypolimnetic anoxia was observed throughout the stratified period, indicating persistent water quality impairment in the deeper zones of this arid-region reservoir.
