The color brine shrimp have is mainly caused by the salinity level of the water body the shrimp are/were living in; this salinity level exerts an effect on the color of brine shrimp in 2 ways.
Brine shrimp live in saline ponds, saline lakes and salt evaporation ponds worldwide. They are filter-feeders and continuously feed themselves with microalgae, bacteria and stirred up detritus. Depending on the salinity of the body of water they are living in different kinds of microalgae will be present as not all species of algae can tolerate higher salinities. Brine shrimp living in ponds having a lower salinity (but still rather high, at least such a high salinity that fish can not survive in it anymore) are generally greenish in color (or have a ‘greenish-bluish’ metallic shine) as there still are plenty of different algae species to feed on in these ponds. But as salinity increases, less and less algae species are able to tolerate the high osmotic pressure exerted by the saline water, and as such higher salinity ponds contain only a couple of algae species anymore. Most of these halophile (which means ‘salt tolerant’) algae species have a red, orange or even purple color, caused by the large amount of betacarotene and other carotenoids these algae produce. Carotenoids help algae to protect themselves from the high light intensities and the accompanying high amount of UV radiation they are subjected to as the water of these high salinity ponds is extremely clear. As less and less organisms can tolerate the high salinity, the water becomes clearer (few other organisms can live in it anymore besides some halophile bacteria and algae). Through the consumption of these algae the brine shrimp obtain the carotenoids and deposit them throughout their body for the same reason algae synthesize carotenoids: to protect themselves against oxidative damage due to the intense UV radiation they are exposed to. Carotenoids are known to be very efficient scavengers of singlet oxygen & peroxyl radicals[1]. So brine shrimp harvested from high salinity ponds have a very red color as pictured below.
[1] Food Lipids - Chemistry, Nutrition and Biotechnology 2nd ed., Marcel Dekker (2002)