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Phenological monitoring is carried out monthly at the 15 Jornada Basin LTER NPP Sites, at which net primary productivity is monitored as part of a long-term study. The sites were chosen to be located in 5 vegetation communities that represent the major vegetation types of the Jornada Basin. These vegetation zones and their associated NPP sites (3 per zone) are: 1) creosotebush scrub (C-CALI, C-GRAV, C-SAND), 2) tarbush flats (T-EAST, T-TAYL, T-WEST), 3) grassland (G-BASN, G-IBPE, G-SUMM), 4) mesquite dunes (M-NORT, M-RABB, M-WELL), and 5) playa (P-COLL, P-SMAL, P-TOBO). Annual estimates of aboveground NPP at these sites, beginning in 1989, are available in data package knb-lter-jrn.210011003.

Each NPP site consists of a 70m x 70m plot in which quadrats are monitored for primary productivity. At most sites there is a buffer zone surrounding the plot that is delineated with corner posts. Phenology monitoring began in 1992 and is done along the west and south side of each NPP site by walking along the outside of the plot with the center of a meter stick held perpendicular to an imaginary line that connects all the buffer zone corner posts. Exceptions: there are no buffers at the three playa sites or at M-NORT, or along the south side of G-SUMM. On these sites the S and W boundaries of the NPP plot itself are walked with the 100cm end of the meter stick touching the outside of the rebar. At P-COLL the E and N boundaries of the NPP plot itself are walked. In January 2001 there was a change in methodology at P-TOBO; the E and S boundaries are walked.

Species of interest falling within this 1 meter wide belt are tallied in one of 5 categories: dormant, non-reproductive (non-rep), in bud, fully open flowers, mature fruits. The most advanced phenological stage present is the one recorded; a plant is considered to be in flower (for example) if there is at least one open flower present (even if the majority of flowers are in the bud stage). Tallies are done in the dot-box method, where each individual is tallied as either a dot or line; 4 dots from corners of a box, and additional counts are represented as lines joining the corners and forming 2 diagonals (completed box with diagonals = count of 10). Each species in a site has its own line on the data sheet. This monitoring results in counts of plants in each of the 5 states, from which percentages can be calculated. In addition, a separate tally for seedlings (defined as plants yet to reach reproductive size) is made. If they survive to reach reproductive size these individuals will eventually be included in the phenological counts.

The monitoring protocol for this study has evolved over time. From 1998 until June 1998 all species encountered were monitored. This proved time consuming, likely magnified observer-to-observer differences, and posed problems for data analysis. Since July 1998 a specific set of species for each site has been monitored, with the total number of species monitored at a given site ranging from 1 to 7. Further refinements to these lists are implemented occasionally to meet research objectives or to provide congruency with other studies.

Certain species of grasses are present in large numbers at some sites. These grasses are measured along a line intercept, as opposed to a belt transect, running between the S and W buffer zone rebars. Each patch or individual of these species that contacts the line is tallied. This method applies to the following grasses at the following sites: Bouteloua eripoda at all sites where it is monitored; Dasyochloa pulchella at C-CALI, C-GRAV, C-SAND and M-RABB; Muhlenbergia arenacea at T-EAST and T-TAYL; Pleuraphis mutica at P-TOBO; Scleropogon brevifolius at G-BASN, T-EAST, T-TAYL, and T-WEST; and Sporobolus airoides at P-TOBO.

Plant tallies can change from month to month due to recruitment and senescence in addition to observer differences. In earlier years if the line-transect method was used for a particular species (such as Dasyochloa pulchella) and the number of individuals dropped consistently to small numbers, it was appropriate to switch back to the belt transect method with approval from the Principal Investigator. Switching between belt and line transects is no longer done. The method column in the data set indicates whether a belt or line transect was used for a species during a given sampling event.

Since 2009 at P-COLL and P-SMAL, the two playa sites where Panicum obtusum is found in dense stands, each square meter (using the meter stick) along the line is checked for reproductive state rather than the entire line being counted as one.