Urine is a primary way to eliminate water-soluble chemicals or their metabolites from the body. Glyphosate is water-soluble, and our kidneys will filter any glyphosate present in the bloodstream prior to elimination via urine.

Humans eliminate glyphosate from their bodies rapidly [1] with little remaining after a few days. This process also applies to naturally occurring chemicals in foods and, knowing this, some researchers study [2] how urine chemistry changes after eating specific foods.
In fact, measurements [3] of caffeine metabolites in wastewater provide a means to estimate caffeine intake at the population level.  

Glyphosate and other pesticides can be present on foods at low levels called residues. Regulatory authorities establish the maximum allowable amount of each pesticide by setting maximum residue levels (MRLs).
An MRL is the highest level of pesticide residue that can legally be present in or on individual crops or foods. MRLs provide a means to determine 1) if a food can be sold, 2) if farmers are following product label instructions, and 3) upper end estimates of dietary pesticide exposures in a population. 

The German non-governmental organization BUND (Association for Environment and Nature Protection―German branch of Friends of the Earth) conducted a study [4] titled “Determination of Glyphosate residues in human urine samples from 18 European countries”.

The majority (56.1%) of the samples did not contain detectable levels of glyphosate, and of the ones that did contain detectable glyphosate, the highest level was still less than two micrograms per litter (two parts per billion). The results translate to an intake that is over 1,000 times lower than what the European Union considers an acceptable daily intake (0.3 mg/kg body weight per day), and more than 3,000 times lower than the equivalent value from the World Health Organization (1.0 mg/kg body weight/day).

These values from EFSA and WHO are exposures that can occur every day throughout a person’s life, without raising concern of risks to human health. The mere detection of glyphosate or other chemicals in urine does not equate with effects on human health [5].