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Nutrient pollution may negatively affect the water quality and ecological status of rivers and estuaries worldwide, specifically in stratified and small inland estuaries. We present a long-term, two-decade data set of dissolved inorganic nutrient concentrations, chlorophyll-<i>a</i> (chl-<i>a</i>), dissolved oxygen (DO), and potentially toxic algal cell concentrations at the Kishon River estuary (Israel) as a case study for assessing nutrient ecological thresholds in such type of estuaries, prevalent along the Mediterranean coast of Israel. In-situ measurements and water samples were collected at 3 permanent stations at the lower part of the estuary every March and October/November in 40 campaigns over the years 2002 to 2021. In spite of an improvement in nutrient loads and concentrations as recorded over the last 2 decades, the nutrient and chl-<i>a</i> levels at the Kishon estuary surface water represent mostly a ‘bad’ or ‘moderate’ ecological state, considering the recommended thresholds discussed in this study. It is suggested to develop a combined suite of nutrient and biological variables for assessing Good Environmental Status (GES), considering the relatively high residence time of such small, low-flow estuarine water bodies.