Many trace metals are essential micronutrients, and all of them can become toxic when they become bioavailable in excess. Bioavailable concentrations of trace metals in the environment and agriculture are vastly different (with natural and anthropogenic causes) in various habitats, ranging from deficient to toxic levels. Therefore, research has focused on response to trace metals by plants and photosynthetic model organisms (algae and bacteria) in terms of uptake, transport, sequestration, speciation, deficiency, toxicity and detoxification. Most early and even numerous recent studies have used environmentally not relevant conditions. This applies in particular to extremely high, environmentally and agriculturally not relevant concentrations of toxic metals and metalloids. Further, individual processes often were not mechanistically interconnected, so that causes and consequences of metal(loid) effects remained unclear. In this contribution, recent insights are shown, mostly in the (sub-)nanomolar range of metal concentrations, with a simulation of natural light- and temperature cycles and trying to interconnect individual effects. The submerged rootless water plant Ceratophyllum demersum turned out to be a useful shoot model, allowing to assess effects on photosynthetic tissues without interaction with root toxicity. In this model it could be shown that metal(loid) (As, Cd, Cr, Cu, Ni) concentrations that were previously considered as not having any effect actually have a strong impact on the plants, and with a different sequence of events than observed at very high concentrations. In addition, Soybean (Glycine max) was used as a model for terrestrial plants and crops. We used a combination of various biophysical and biochemical methods for measurements in vivo (e.g. photosynthesis biophysics, formation of reactive oxygen species, metal transport), in situ (e.g. quantitative (sub)cellular distribution and speciation of metals, mRNA levels) as well as on isolated proteins (for identification and characterization of metalloproteins) and metabolites (metabolomics). For example, using metalloproteomics via HPLC-ICPMS of protein extracts from stressed plants, changes in target sites of metal binding to proteins from deficient to toxic concentrations could be analyzed. X-ray absorption (XANES) and fluorescence (µXRF) provided information about metal(loid) speciation and distribution. The combination of techniques clearly showed metal(loid)-induced changes in the metabolism, already at very low concentrations, and allowed for new insights into the mechanisms of sublethal toxicity of As, Cd and Cu.