Scarcity of stream salinity data poses a challenge to understanding salinity dynamics and its implications for water supply management in water-scarce salt-prone regions around the world. This paper introduces a framework for generating continuous daily stream salinity estimates using instance-based transfer learning (TL) and assessing the reliability of the synthetic salinity data through uncertainty quantification via prediction intervals (PIs). The framework was developed using two temporally distinct specific conductance (SC) datasets from the Upper Red River Basin (URRB) located in southwestern Oklahoma and Texas Panhandle, United States. The instance-based TL approach was implemented by calibrating Feedforward Neural Networks (FFNNs) on a source SC dataset of around 1200 instantaneous grab samples collected by United States Geological Survey (USGS) from 1959 to 1993. The trained FFNNs were subsequently tested on a target dataset (1998-present) of 220 instantaneous grab samples collected by the Oklahoma Water Resources Board (OWRB). The framework's generalizability was assessed in the data-rich Bird Creek watershed in Oklahoma by manipulating continuous SC data to simulate data-scarce conditions for training the models and using the complete Bird Creek dataset for model evaluation. The Lower Upper Bound Estimation (LUBE) method was used with FFNNs to estimate PIs for uncertainty quantification. Autoregressive SC prediction methods via FFNN were found to be reliable with Nash Sutcliffe Efficiency (NSE) values of 0.65 and 0.45 on in-sample and out-of-sample test data, respectively. The same modeling scenario resulted in an NSE of 0.54 for the Bird Creek data using a similar missing data ratio, whereas a higher ratio of observed data increased the accuracy (NSE = 0.84). The relatively narrow estimated PIs for the North Fork Red River in the URRB indicated satisfactory stream salinity predictions, showing an average width equivalent to 25 % of the observed range and a confidence level of 70 %.