In order to comprehend the groundwater nitrate contamination in Hainan Island, which is recognized as China's sole “tropical agricultural production base,” the distribution characteristics of nitrate in different aquifers and land-use types were elucidated through hydrochemical and geostatistical analysis methods. Principal component analysis (PCA), hierarchical cluster analysis (HCA), and absolute principal component score-multiple linear regression (APCS-MLR) were employed for qualitative and quantitative analysis of the nitrate source. The results showed that NO3−-high (>88.57 mg/L) groundwater accounted for about 10 % of the total distribution area of the western coastal area in Hainan Island. Moreover, the proportions of NO3−-high groundwater in pore water and fissure water were 10 % and 7 %, respectively. The order of groundwater nitrate concentration in different land-use types was as follows: bare land, cultivated land, construction land, grassland, and woodland. The main sources of elevated nitrate concentrations in pore water were animal feces and nitrogen/potassium fertilizers, accounting for 45.4 % of the overall contribution. These substances infiltrated through the vadose zone, leaching out and mobilizing selenium within this zone, ultimately leading to the characteristic enrichment patterns observed in pore water, including nitrate, arsenic, potassium, and selenium. Furthermore, the occurrence of high nitrate in fissure water was mainly attributed to the leaching of cultured manure, septic tank leakage, and infiltration of domestic sewage, accounting for a contribution rate of 32.9 %. Simultaneously, under oxidizing conditions, selenium became activated and entered groundwater through water flow, thereby exhibiting common enrichment characteristics with nitrate and potassium in fissure water. In addition, the assessment of human health risks revealed that 16 % and 40 % of groundwater samples posed unacceptable non-carcinogenic risks to adults and children respectively, with a higher risk for local children. The study recommends the reasonable application of chemical fertilizers, as well as the strengthening of sewage treatment capacity and standardized disposal of manure and feces, to reduce nitrate contamination of groundwater at source and ensure the safety of drinking water.