Storm water runoff is the main contributor to non-point source (NPS) pollution in agricultural land. This issue is extremely important in tropical region due to its high intensity and frequent storms. The objectives of this study were to determine the crop coefficient of two vegetable crops – bittergourd (Mormordica Charantia) and chilli (Capsicum Annuum), investigate the mechanism of NPS pollutant transport and the influence of hydrologic regime on the pollutant loading. This study was conducted at the Modern Agriculture Centre in Kluang, Johor, from August 2013 to May 2014. A total of 86 rainfall events were recorded but only 52 storms had generated measurable runoff. Samples of runoff, soil water and groundwater were collected after every rainfall event and analysed for nutrient and sediment contents. Twenty-six reference evapotranspiration (ETo) models which were classified into four different groups were employed and their performance was ranked based on eight different statistical test. Penman model provide the best result in estimating ETo while the Schendel model tended to overestimate the observed pan ET. The limited parameters used in the temperature based group causes poor performance in predicting the ETo values. Crop coefficient (Kc) curves for both crops were developed as the ratio of actual ET measured by minilysimeters to the ET values of the best model. The Kc values for the bittergourd were 0.58, 0.88 and 0.69 while for chili were 0.58, 0.95 and 0.73 for the initial, mid and end growth stages, respectively. More runoff event was observed for the bittergourd as its growing period coincided with the North-East Monsoon. The average runoff-rainfall ratio is less than one percent due to the high hydraulic conductivity of the site. The concentrations of nutrients and sediments were very high with maximum Nitrite (NO2), Nitrate (NO3), Ammoniacal-Nitrogen (NH3-N), Phosphate (PO4), Total Nitrogen (TN), Total Phosphorus (TP), Chemical Oxygen Demand (COD) and Total Suspended Solids (TSS) concentrations in the runoff were 0.385, 10, 4.2, 13.7, 27, 18, 190 and 15000 mg/l respectively. However, the calculated pollutant loading were low due to the remarkably small surface runoff volume. Soil water analysis at 15 and 60 cm soil depth shows a high Phosphorus (P) element leaching to the deeper depth even though P is less mobile. Nitrate concentration showed an increasing trend compared to other nutrients with a maximum of 1.7 mg/l at the end of the study period. The calibration and validation of the Root Zone Water Quality Model (RZWQM2) were carried out to model the leaching of NO3 to the groundwater. The results of this study can be applied to formulate more reliable water management schemes based on the water requirement of the vegetable crops and providing new information for controlling NPS pollution loading from agricultural activities