The impact of the constituent oxides of nitrogen, carbon, sulphur, and other particulate matter which make up the gas emissions from diesel engines has motivated several control techniques for these pollutants. Water-in-diesel emulsions provide a reliable solution, but the wear effects on the fuel injection system (FIS) still pose remarkable concerns. Because pressure signals from the common rail (CR) reflect the dynamics associated with varying emulsion compositions and at varying engine RPMs, an investigative (and diagnostic) study was conducted on a KIA Sorento 2004 four-cylinder line engine at various water-in-diesel emulsion compositions and engine speeds. Alongside visual/microscopic inspections and spectral analyses, the diagnostic framework proposed herein functions on the use of standardized first-order differentials of the CR pressure signals to generate reliable continuous wavelet coefficients (CWCs) which capture discriminative spectral and transient information for accurate diagnosis. The results show that by extracting the CWCs from the first-order CR pressure differentials up to the 512th scale on a Mexican hat wavelet, adequate fault parameters can be extracted for use by a deep neural network (DNN) whose hyperparameters were globally optimized following a grid search. With a test accuracy of 92.3% against other widely-used ML-based diagnostic tools, the proposed DNN-based diagnostics tool was empirically assessed using several performance evaluation metrics.