Fast detection of contaminants of emerging concern (CECs) in water resources is of great environmental interest. Ideally, sustainable materials should be used in water quality monitoring technologies implemented for such purposes. In this regard, the application of bio-based materials aimed at the fabrication of analytical platforms has become of great importance. This research merges both endeavors by exploring the application of chitosan-coated paper, decorated with silver nanoparticles (AgNPs), on surface-enhanced Raman scattering (SERS) spectroscopy studies of two distinct types of CECs dissolved in aqueous samples: an antibiotic (ciprofloxacin) and a pesticide (thiram). Our results indicate the superior SERS performance of biocoated substrates compared to their non-coated paper counterparts. The detection limits achieved for thiram and ciprofloxacin using the biocoated substrates were 0.024 ppm and 7.7 ppm, respectively. The efficient detection of both analytes is interpreted in terms of the role of the biopolymer in promoting AgNPs assemblies that result in local regions of enhanced SERS activity. Taking advantage of these observations, we use confocal Raman microscopy to obtain Raman images of the substrates using ciprofloxacin and thiram as molecular probes. We also demonstrate that these biobased substrates can be promising for on-site analysis when used in conjunction with portable Raman instruments.