Monitoring of water ecosystems, especially rivers, represents an exceptionally complex task, due to the fluctuating discharges and continuous water movements, with the consequent need to consider either the temporal dynamics in the parameters analysed or time-integrated measures. Even if chemical analyses of water and/or sediments allow obtaining challenging and expensive information on concentration gradients, the actual pollutant bioavailability cannot be ascertained without taking into account the aquatic biota. Biomonitors, providing space- and time-integrated information on environmental quality, allow cheaply and accurately detecting the actual availability, mobility, transfer through the food webs and fate of pollutants in the aquatic environment over a wide range of concentrations. Among biomonitors, selected aquatic autotropic organisms act as effective bioaccumulators, which continuously absorb and accumulate pollutants from sediments and water, integrating pollution peaks, without detectable effects on physiological functions and with pollutant concentrations in their biomass linearly related to their exposure time. The current legislations on the topic, like the EU Water Framework Directive, boosted the application of biomonitoring in the evaluation of aquatic ecosystem quality and strengthened the use of aquatic plants in river quality assessment. Identifying vascular plants as nutrient and non-essential element accumulators for passive biomonitoring (using native organisms) of both urban and remote rivers is a challenging task, especially in the Mediterranean area, where the particular climate determines severe variations in river hydrology. Thanks to several years of research, we validated various candidate passive biomonitors of potentially toxic elements for this area and performed extensive biomonitoring studies using the roots (Helosciadium nodiflorum and Mentha aquatica) or the shoots (Potamogeton pectinatus) of cosmopolitan species growing along the urban Irno and Sarno rivers and along the remote Bussento and Calore Salernitano rivers (southern Italy). Notwithstanding the expected different accumulation degree among the species, they allowed obtaining clear and detailed spatial concentration gradients, either attributable to anthropogenic impacts or to natural peculiarities. However, to overcome the limitations imposed by the spatial distribution of passive bioaccumulators, we expanded our research also to active biomonitors (transferred organisms), validating novel species and developing effective exposure devices. Apart from the opportunity to monitor areas lacking native bioaccumulators, this choice reduces sample variability and allows precise timings of exposure and the derivation of accurate mean accumulation rates. In particular, our researches allowed validating the macrophytic alga Chara gymnophylla as a novel active biomonitor of potentially toxic elements and, in combination with a long-established biomonitor, the aquatic moss Fontinalis antipyretica, deriving clear contamination scenarios in sensitive areas, with indications of the alleged sources.