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The relationships between chlorophyll a concentration and environmental (climatic and associated hydrographical) factors were investigated in the estuary of Urdaibai (Bay of Biscay) in different salinity zones of the euhaline region, using time-series for the period 1997–2006. Transfer function (TF) models were used on quarterly data (3 month mean values) to establish possible relationships between time-series. In the non-nutrient limited waters with salinities of 30 and 33 PSU, a chain of effects from the North Atlantic Oscillation (NAO) to chlorophyll a was established, where air temperature followed inversely the NAO index, water temperature followed air temperature and chlorophyll a followed water temperature. Each of the steps occurred with a lag of 0 (within the 3 month period); however, the effect from NAO to chlorophyll a showed a lag of 1 (a mean of 3 months delay). Consistent with this result, annual mean chlorophyll a biomass in the 30 and 33 PSU salinity zones showed a significant positive relationship with annual mean water temperature and a significant negative relationship with the 12 month mean NAO index from October of the previous year to September. In the 35 PSU salinity zone, no significant relationship between chlorophyll a and NAO or water temperature was observed. It is suggested that nutrient limitation distorts the effect of temperature on phytoplankton biomass enhancement in the outer estuary (35 PSU salinity zone). [ABSTRACT FROM AUTHOR]