Accurate and sufficient water quality data is essential for watershed management and sustainability. Machine learning models have shown great potentials for estimating water quality with the development of online sensors. However, accurate estimation is challenging because of uncertainties related to models used and data input. In this study, random forest (RF), support vector machine (SVM), and back-propagation neural network (BPNN) models are developed with three sampling frequency datasets (i.e., 4-hourly, daily, and weekly) and five conventional indicators (i.e., water temperature (WT), hydrogen ion concentration (pH), electrical conductivity (EC), dissolved oxygen (DO), and turbidity (TUR)) as surrogates to individually estimate riverine total phosphorus (TP), total nitrogen (TN), and ammonia nitrogen (NH4+-N) in a small-scale coastal watershed. The results show that the RF model outperforms the SVM and BPNN machine learning models in terms of estimative performance, which explains much of the variation in TP (79 ± 1.3%), TN (84 ± 0.9%), and NH4+-N (75 ± 1.3%), when using the 4-hourly sampling frequency dataset. The higher sampling frequency would help the RF obtain a significantly better performance for the three nutrient estimation measures (4-hourly > daily > weekly) for R2 and NSE values. WT, EC, and TUR were the three key input indicators for nutrient estimations in RF. Our study highlights the importance of high-frequency data as input to machine learning model development. The RF model is shown to be viable for riverine nutrient estimation in small-scale watersheds of important local water security.