Observations taken in Loch Linnhe, a fjord on the west coast of Scotland in 1992, indicate that nutrient distributions are controlled by physical mixing processes (conservative behaviour), temporally varying end-member concentrations (apparently non-conservative behaviour) and biogeochemical processes (real non-conservative behaviour). One-dimensional steady-state mixing diagrams conventionally employed for estuarine nutrient studies cannot be used for Loch Linnhe because of the complex hydrography observed. A one-dimensional box model has been developed which accurately reproduces the hydrography of the system and has been used to isolate and quantify the different types of nutrient behaviour in the system: non-conservative behaviour is identified in the isolated bottom-waters of the basin and apparently non-conservative behaviour is identified at depths greater than 60 m. Chlorophyll data show the onset of a phytoplankton bloom coinciding with a deep water renewal event. A similar sequence of events was also noted in 1990 and 1991 and it is suggested that these events are linked.