The Mediterranean climate is characterized by extended dry and wet periods with a regime of irregular precipitation. Watersheds in the area, especially in the island area of the Aegean Sea, are typically small and drained by temporary rivers and streams. Temporary waters are unique and sensitive ecosystems as well as important components of the local hydrologic systems. In many Mediterranean coastal areas, they are responsible for the total amount of inflow water to the sea and directly associated with most coastal water nutrient balance and quality problems. As a consequence of the climatic changes and the increasing anthropogenic pressures, temporary rivers are expected to encounter longer dry periods and a higher variability that may have a significant effect on those sensitive systems. With regard to the requirements of the European Water Framework Directive, there is a need to better define the quality characteristics of temporary waters and to evaluate the essential features of those river systems in terms of their seasonal variability in nutrient transport. This will contribute to a better understanding, prediction and management of the complex processes of interaction between temporary flowing waters and receiving water bodies in the future. The present research uses both field measurements and laboratory analyses for the assessment of water quality regarding the nutrient transport in a small eastern Mediterranean watershed. The field work supplied the rate of flow, in situ parameter measurements and water sampling from nine sampling locations representative of the hydrographic network. Physical parameters such as pH, temperature, conductivity, and dissolved oxygen were measured directly in the field during sampling. Chemical analysis of the collected samples was performed using spectrophotometry methods to estimate the nutrient load. The temporal distribution of NO2- -N, NO3- -N, NH3 -N and PO4- -P concentration was found to be closely related to the seasonal flow variations. Low values of nutrient concentrations were observed during dry periods, while they reached their maximum annual values during rainy periods. NO3- was found to be the dominant form of DIN (Dissolved Inorganic Nitrogen) in the study area, with few occasional exceptions. The contribution of individual sub-watersheds in water and nutrient loads to the main river was found to be in coherence with the size of the drainage area, the slope and the existence of water springs. Nutrient load in individual sub-watersheds also varied along their route according to a diversity of factors, mainly of anthropogenic origin. The olive cropping methods, light urban wastes, farm wastes and the few olive mills in the area were found to have a significant effect in nutrient spatial and temporal distribution within the watershed. The study results may be indicative of the expected nutrient dynamics and outflow from a small agricultural Mediterranean watershed.