Phenotype is often discussed at a fairly coarse level. In biology classes we ponder simple genotypes from Mendelian genetics, and discern that the pea plant with the YY genotype bears yellow pea seeds.
Consider a suspension of tumor cells being grown in a petri dish, however. A fairly straightforward way to asses the phenotype of the cells is by confocal microscopy
Say you grow the same cells, but some at normal oxygen and some at lower oxygen. Refer to the following figure:
In B, the investigators are using fluorescent antibody label, as you'd use in flow cytometry, to perform confocal microscopy. At 1% oxygen for up to 21 days, the phenotype of the same cells profoundly differ (reference). Flow cytometry can also be used to identify difference in phenotype that arise from environmental factors.
Take for example T cells isolated from you blood. I can change the phenotype based on surface receptors detected from flow cytometry, by adding different cytokines to the culture medium. If I add interleukin-12, I'm most likely to differentiate my T cells to discernibly type-1 helper or cytotoxic cells. I can tell due to the presence or absence, or abundance of markers such as CCR5 or CXCR3.
And if you sequence these cells, you get the same material. Epigenetic changes are harder to wrap your head around. In the hypoxia example, the lack of oxygen is thought to change the phenotype by modifying the way the cell machinery can access and express key genes associated with the hypoxia phenotype.
The take home point here, is that in order to discern the techniques that are available to you, it's important to define the system you're researching. For example, I have no idea how they determine the environmental impact on animal species. But, I can sit here and rattle off techniques to analyze single cells or systems of cells.