Phalaris aquatica is known to cause toxicity in livestock in the form of acute or chronic staggers or sudden death neurological (SDN) syndrome. Breeding of cultivars that produce lower concentrations of suspected alkaloid toxins has been conducted, but these cultivars continue to cause staggers and SDN toxicity. Field samples of grazed phalaris pasture were collected during one growth season (February–June 2016), and from pastures where cases of staggers and/or SDN had occurred in previous years, and immediately after two cases of toxicity. Pasture collected from a paddock where a case of SDN occurred 4 days prior had elevated levels of 5-methoxy-N,N-dimethyltryptamine (5-MeO DMT) and slightly elevated levels of dimethyltryptamine (DMT) compared with other collections from the region. Pasture collected from a paddock at the time of a case of phalaris staggers did not have elevated levels of the quantified alkaloids. Across the measurement period, potentially toxic alkaloids gramine, hordenine, DMT and 5-MeO DMT were observed to decrease in concentration, whereas β-carboline (norharmane) was not detected in any sample. Excessive drying out of dormant plants was hypothesised to be a risk factor for phalaris toxicity. Continued management of potentially toxic phalaris pasture could include measures to manipulate the physiological processes that result in increased toxic alkaloids, including methods to reduce drying out of dormant phalaris plants, and managing stocking rates and grazing species to mitigate potential toxicity.