Biodiversity monitoring holds great importance in both ecological research and resource management, serving as an enabling tool for understanding and preserving ecosystems. The integration of molecular tools to biodiversity monitoring enhances researchers' capabilities, contributing to a deeper understanding of patterns and ecosystem processes. Here, I expand the limits of biodiversity monitoring by contributing to the detection and interpretation of information obtained from two biological molecules recovered from environmental samples: DNA and Proteins. In the first three chapters of my thesis, I address the spatial resolution of environmental DNA (eDNA) in flowing waters. Environmental DNA is a powerful monitoring tool based in detecting organisms remotely by capturing the DNA they passively release into the environment. Despite its rapid increase in popularity, many questions remain regarding the “ecology” of eDNA, which is defined as the origin, state, fate, and transport of the molecules. Notably, most eDNA ecology experiments are performed without considering eDNA`s heterogeneous composition, usually quantifying total eDNA. Additionally, less is known about flowing water systems, where particles and eDNA are also transported downstream and subject to the dynamics of substrate trapping and resuspension. Here, I significantly expand our knowledge of eDNA ecology, providing insight into how eDNA transforms over space and time, how it interacts with other components of the environment, and how we may use this information in our favor when interpreting eDNA data. Despite eDNA being the standard for remote detection, organisms leave behind other molecules that could be used for the same purpose. Accordingly, I also explore the use of an environmental protein (eProtein) for the detection of an organism. Specifically, I use δ-endotoxins from Bacillus thuringiensis, a toxin commonly introduced into Genetically modified organisms, as a model to explore the use of eProteins for monitoring. First, I explore the fate of this proteins in streams, a system in which they have been found in significant concentrations, and where they might impact off-target organisms. Second, I explore the application of light transmission spectroscopy and functionalized gold nanoparticles to develop a novel field-ready method of eProtein detection. The developed method has higher sensitivity than competing field methods.