This study evaluated the quality of drinking water in 20 rural communities of Puerto Limón parish, located in Santo Domingo de los Tsáchilas province, Ecuador, through physicochemical and microbiological analyses conducted during two climatic seasons in 2023. A total of 163 samples were collected per season from both surface and groundwater sources, at intake and household distribution points. The parameters analyzed—temperature, pH, free residual chlorine, mono-chloramines, turbidity, color, nitrates, nitrites, fluorides, fecal coliforms, total dissolved solids (TDS), and electrical conductivity—were compared with the values established in the national standard NTE INEN 1108:2020. Marked variations were found among communities and between seasons. TDS and conductivity exhibited high values during the dry season. At the same time, turbidity, color, nitrates, and fluorides increased with rainfall. Conversely, median concentrations of free chlorine and monochloramines consistently remained below the quantification limit. Finally, microbiological analysis yielded values for fecal coliforms that exceeded 2400 MPN/100 mL in some samples. Statistical analysis confirmed a non-normal data distribution (Lilliefors test), significant seasonal differences in nine parameters (Wilcoxon-Pratt test), and a strong correlation between TDS and conductivity (Kendall’s Tau), along with weaker associations between turbidity, pH, nitrates, and color. The findings highlight the influence of seasonality and water source type on water quality and support the need for ongoing monitoring in rural areas without treatment systems. As one of the first systematic studies in this region, this work constitutes a notable technical-scientific contribution to the local community.