<p>This study aims to evaluate the spatial variation of water quality in three short rivers on Penang Island in relation to tidal dynamics and seawater intrusion from the Strait of Malacca. Sungai Tukun, located within a national park, served as a reference site. Ten sampling stations were established across upstream, midstream, and downstream segments of the rivers, with an additional site in Sungai Batu Ferringhi to capture anthropogenic influences. Water sampling and in situ measurements were conducted during spring and neap tides and analysed using the standard method (APHA, 2017). The Kruskal–Wallis H test revealed significant spatial variations (<i>p</i> &lt; 0.05) in multiple parameters, including pH, total dissolved solids, salinity, Secchi depth, ammonium, nitrate, chlorophyll-a, orthophosphate, and discharge. The Mann–Whitney <i>U</i> test showed significant differences (<i>p</i> &lt; 0.01) in water temperature, pH, salinity, total dissolved solids, ammonium, discharge, and euphotic depth between high and low tides at downstream stations. Significant vertical stratification in salinity and Secchi disk depth was also observed at downstream segments (<i>p</i> &lt; 0.01). Principal component analysis (PCA) indicated that PC1, dominated by salinity, water temperature, and total dissolved solids, accounted for 28.80%, 30.88%, and 27.02% of the total variance in Sungai Batu Ferringhi, Sungai Tukun, and Sungai Keluang, respectively, indicating tidal influence. PC2 was mainly associated with nutrient-related variables. The findings revealed distinct spatial variation in water quality and nutrient distribution among the three short rivers of Penang Island, with tidal dynamics contributing to these patterns and informing sustainable freshwater management in tidal-influenced catchments.</p>