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Abstract: Storm runoff in the steep watersheds in Hawaii leads to sediment and freshwater pulses to coastal waters that quickly affect nearshore water quality. This is particularly true in semi-enclosed embayments, such as Kaneohe Bay, Oahu, where water has a relatively long residence time compared to more open coastal areas of the islands. In this paper the authors discuss water quality and productivity in Kaneohe Bay after back-to-back rain events in late November and early December 2003, following a particularly dry summer. The short-term biogeochemical response of coastal waters and the ecosystem to runoff and physical forcing was evaluated through a combination of continuous in situ measurements and adaptive synoptic sampling carried out on a variety of temporal and spatial scales. Dissolved N:P ratios in Kaneohe Bay, which normally range from 2 to 4, consistent with a previously documented N-limited system, increase to as high as >25 during storm runoff. Order of magnitude increases in nutrients and chlorophyll in the bay shortly after the first storm and subsequent changes in the plankton community structure reflect an evolving biological response stimulated by storm inputs to the bay. Phytoplankton blooms did not draw nutrients down to limiting levels, likely due to grazing pressure by zooplankton, yet phytoplankton were not grazed to limiting levels. As a result, a slow but steady increase of the phytoplankton standing stock was observed over time. Low phosphate levels (<0.2μM) combined with very high N:P values are typical in Kaneohe Bay waters after most storms and P often becomes the ultimate limiting nutrient. Prior to and after the November–December 2003 storms, however, dissolved P remained near or above 0.3μM, implying that the system never became P limited and suggesting particle buffering of P concentrations. Furthermore, concentrations of NH3 became elevated (8–16μM) following the initial storm, first in deep and subsequently in surface waters, and remained high for several months. Remineralization of organic matter transported into southern Kaneohe Bay during the storm possibly contributes nutrients that sustain phytoplankton productivity for extended periods. [Copyright &y& Elsevier]