The Class A1 uses are assessed (monitored) as "partially supported" based on results of monitoring for indicator bacteria (E. coli) during recreational seasons of 2012 through 2014. The geometric means of indicator bacteria (E. coli) in the 22 samples collected during the recreational seasons of 2012 through 2014 at DNR station 10850003 upstream from Ames were as follows: the 2012 geometric mean was 46 orgs/100 ml, the 2013 geometric mean was 94orgs/100 ml, and the 2014 geometric mean was 223orgs/100 ml. Only the 2014 geometric means exceeded the Class A1 criterion of 126 orgs/100 ml; the 2012 and 2013 geometric means werewell below the criterion. Seven of the 22 samples (32%) exceeded the Class A1 single-sample maximum criterion of 235 orgs/100 ml. According to U.S. EPA guidelines for Section 305(b) reporting and DNR’s assessment/listing methodology, if a recreation season geometric mean exceeds the respective water quality criterion, the contact recreation uses are "impaired" (see pgs 3-33 to 3-35 of U.S. EPA 1997b). Thus, because at least one recreation season geometric mean exceeded criteria for Class A1 uses, these uses are assessed as “impaired.”

The results of biological monitoring in 2013 and 2014 suggest “partial support” of the aquatic life uses of this river segment. A series of biological metrics which reflect stream water quality and habitat integrity were calculated from the biological sampling data. The biological metrics are based on the numbers and types of fish species and benthic macroinvertebrate taxa that were collected in the stream sampling reach. The biological metrics were combined to make a fish community index of biotic integrity (FIBI) and a benthic macroinvertebrate community index of biotic integrity (BMIBI). The indices rank the biological integrity of a stream sampling reach on a rising scale from 0 (minimum) to 100 (maximum). The 2013 FIBI score was 13(poor) and the BMIBI scores were 41 (fair) and 56, 63 (both good). The 2014 BMIBI scores were 38, 53 (both fair). The aquatic life use support was assessed as partially supporting (=PS), based on a comparison of the FIBI and BMIBI scores with biological impairment criteria (BIC) established for previous Section 305(b) reports. The non-riffle habitat FIBI BIC for this ecoregion is 32 and the BMIBI BIC for this ecoregion is 62. This segment failedthe FIBI BIC one time in 2013 and passed the BMIBI BIC 1/5 times in the last five years. The biological impairment criteria were determined from a statistical analysis of data collected at stream ecoregion reference sites from 1994-2008.

This aquatic life assessment is now considered "monitored" based on a change in the 2010 DNR assessment methodology. DNR now requires a segment have two or more biological samples collected from the segment in multiple years over a five-year period to be considered “monitored”. This segment had multiple BMIBI samples collected in the previous five years.

The Class B(WW-1) (aquatic life) uses are assessed (monitored) as "partially supported" due to the occurrence of a fish kill near Story City in August 2011. The kill occurred on or before August 4, 2011. Approximately 27,400 fish were killed over five miles of stream. The value of the fish was reported as $38,056.16; the cost of the DNR investigation was $1,928.83. The cause of the kill was identified as animal waste from a hog confinement.

According to DNR’s assessment/listing methodology, the occurrence of a single pollutant-caused fish kill, or a fish kill of unknown origin, on a waterbody or waterbody reach during the most recent assessment period indicates a severe stress to the aquatic community and suggests that the aquatic life uses should be assessed as “impaired.” If a cause of the kill is identified, and the cause is either known, or suspected, to be a “pollutant”, the assessment type is considered “monitored” and the affected waterbody is a candidate for Section 303(d) listing. Fish kills attributed to a pollutant, but where a source of the pollutant was not identified and/or where enforcement actions were not taken against the responsible party, will be placed into Integrated Report subcategory 5b. The intent of placing these waterbodies into Category 5 is not to necessarily require a TMDL but to keep the impairment highlighted due to the potential for similar future kills from the unaddressed causes and/or sources. If, however, a consent order has been issued to the party responsible for the kill and monetary restitution has been sought for the fish killed, the affected waterbody will be placed in IR Category 4d (impaired but TMDL not required). DNR records show that the party responsible for the kill was identified and DNR sought and received restitution for the value of the fish killed and the costs incurred by DNR during investigation of the kill. Thus, this assessment segment was placed in Category 4d of Iowa’s 2014 and 2016 Integrated Reports.For IR Category 4d waters (i.e., a fish kill-impaired water where enforcement actions were taken against the party responsible for the kill), if no additional fish kills have been reported over at least five years subsequent to the kill, any impact from the fish kill upon which the impairment was based likely has long-ago dissipated. The IR category for the kill will be changed from 4d to 3b (potentially impaired) and added to the state list of waters in need of further investigation. The 2011 fish kill in this segment was moved to Category 3b for this (2018) IR cycle.

Despite the indications of impairment suggested by the August 2011 fish kill, results of both chemical/physical water quality monitoring suggest relatively good quality conditions in this segment of the South Skunk River. Results of chemical/physical water quality monitoring during the 2010-12 period at the DNR ambient station upstream from Ames showed no violations of Class B(WW1) water quality criteria for dissolved oxygen, pH, ammonia-nitrogen, temperature, chloride, or sulfate in the 36 samples collected. These results suggest “full support” of the Class B(WW1) aquatic life uses.

Fish consumption remain assessed (evaluated) as "fully supported" based on results of U.S. EPA/DNR fish tissue (RAFT) monitoring conducted in 2004 near Story City. Because these data are now more than five years old, and because as data age beyond five years they are less able to represent current water quality conditions, the assessment type is changed from “monitored” (a higher confidence assessment) to “evaluated” (lower confidence assessment.) The composite samples of fillets from common carp and smallmouth bass had low levels of contaminants. Levels of primary contaminants in the composite sample of common carp fillets were as follows: mercury: 0.069 ppm; total PCBs: 0.09 ppm; and technical chlordane: 0.031 ppm. Levels of primary contaminants in the composite sample of smallmouth bass fillets were as follows: mercury: 0.109 ppm; total PCBs: 0.09 ppm; and technical chlordane: < 0.03 ppm. The existence of, or potential for, a fish consumption advisory is the basis for Section 305(b) assessments of the degree to which Iowa’s lakes and rivers support their fish consumption uses. The levels of contaminants in the fish tissue samples collected in 2004 do not exceed any of Iowa’s advisory trigger levels, thus suggesting no justification for issuance of a consumption advisory for this waterbody.