Comprehending the intricate ecosystem dynamics and rapid changes in the global environment is important in light of the continuous loss of biodiversity and the widespread effects of anthropogenic contamination. Conventional approaches frequently entail invasive sampling, which can injure organisms, disturb ecosystems, and restrict long-term research, emphasizing the need for noninvasive substitutes. The development and application of effective, practical, and noninvasive assessment methods has become a top goal in ecological and environmental research towards sustainable management. This research investigates the possibilities of using fish scales and plant leaves as robust yet convenient noninvasive tools for ecology and ecosystem health research. The study carried out scale elemental analysis of various fish species from fresh freshwater, coastal, and freshwater-brackish water-marine water environments. The deposition of microplastics and elements in plant leaves was investigated along an urbanization gradient from industrial, residential, and rural areas. The study revealed that scale elements have an association with the environment of fish habitat and feeding ecology. The bottom-dwelling fish (i.e., demersal) accumulate sediment-associated elements such as Cu, Fe, S, Sr, etc., in higher concentrations. Fish living in the water column (i.e., pelagic) acquire primarily water-dissolved elements and metals from their planktonic prey, like Ca, K, Mn, Zn, etc. Higher trophic, predatory fish (i.e., carnivorous) accumulate elements including As, Cu, Hg, Ni, etc. through biomagnification, opposite to their lower trophic counterparts (herbivorous). Additionally, the scale element ratios, particularly the Sr/Ca, Mn/Ca, and Ba/Ca ratios, have been found to show potential signatory indications of fish habitat. Therefore, it concerns their dwelling habitat and the source of food, which is to be incorporated into the fish scales. It indicated that fish scales can be employed as a non-invasive tool for deciphering fish life history and ecology without endangering the fish. Similarly, higher concentrations of microplastics and metals were found in plant leaves with an increasing degree of urbanization, mirroring anthropogenic impacts in different areas. Leaves of Polyalthia longifolia were found to accumulate high concentrations of PTE-type microplastics along an industrial–residential–rural gradient in Bangladesh. P. longifolia can accumulate Cd, Pb, and Zn in high concentrations in its leaf tissues. The pollution index for Cd indicated a moderate level of pollution in the rural area, considerable pollution in the residential area, and very high pollution in the industrial area. It reflects the potential of the P. longifolia plant leaves, which are a good bioindicator and suitable to be used for biomonitoring studies. The findings demonstrate the fascinating potential of fish scales and plant leaves as promising noninvasive tools for ecological and environmental monitoring. The simultaneous use of these two methods, aquatic signals trapped in fish scales and terrestrial impulses recorded by plant leaves, offers an exceptionally thorough and non-destructive lens for ecological and environmental monitoring.